schrodinger.application.phase.packages.shape_generator module¶

Supplies consistent means of generating shape structures via ligand and pharmacophore command line options.

class schrodinger.application.phase.packages.shape_generator.AtomTypes¶

Bases: enum.Enum

An enumeration.

class schrodinger.application.phase.packages.shape_generator.ShapeGenerator(args)¶

Bases: object

getGenerationOptions()¶

Populates ShapeGenerationOptions object from ShapeGenerator members

Returns:	shape generation options object
Return type:	shape.ShapeGenerationOptions

getFeatureDefinitions(args)¶

Collects the feature definitions to use for generating pharmacophore hypothesis shapes from ligands.

Parameters:	args (argparser.Namespace) – argument namespace with command line options
Returns:	list of pharmacophore feature definitions
Return type:	list of phase.PhpFeatureDefinition

getHypothesisFeatureRadii(radii_file)¶

Collects user specified pharmacophore feature radii to use for generating pharmacophore hypothesis shapes from ligands.

Parameters:	radii_file (str) – user supplied .rad filename
Returns:	Data for feature specific radii
Return type:	phase.PhpFeatureData

getHypothesisSitesShape(sites)¶

Returns a shape structure created from the given Phase hypothesis.

Parameters:	sites (list(phase.PhpSite)) – pharmacophore sites source
Returns:	shape structure derived from the given hypothesis
Return type:	shape.ShapeStructure

getShape(st)¶

Creates a shape structure from the given ligand structure.

Parameters:	st (structure.Structure) – ligand source structure
Returns:	shape structure derived from the given structure
Return type:	shape.ShapeStructure

getConformerShapes(conformers)¶

Creates a list of shape structure from the given ligand conformers.

Parameters:	conformers (list(structure.Structure)) – ligand source conformers of the same structure
Returns:	shape structures derived from the given conformers
Return type:	list(shape.ShapeStructure)

schrodinger.application.phase.packages.shape_generator.add_ligand_options(parser)¶

Adds ligand-based screening options to the provided parser.

Parameters:	parser (argparser.ArgumentParser) – Argument parser object

schrodinger.application.phase.packages.shape_generator.add_pharmacophore_options(parser)¶

Adds pharmacophore-based screening options to the provided parser.

Parameters:	parser (argparser.ArgumentParser) – Argument parser object

schrodinger.application.phase.packages.shape_generator.validate_shape_gen_options(args)¶

Validates command-line argument pharmacophore option compatibility.

Parameters:	args (argparse.Namespace) – argument namespace with command line options
Returns:	tuple of validation success, and error message
Return type:	bool, str